Updated 2019-07-15

Run CDO on the Cluster

Overview

  • Climate Data Operators is a collection of command-line operators to manipulate and analyze climate and numerical weather prediction data.
  • This guide will cover how to run CDO on the Cluster.
  • More information about CDO can be found on their homepage.

Summary

  • There are various operators for you to use that can be viewed with cdo -h after loading the necessary modules.
  • For this walkthrough, we will cover basic operations such as displaying variables, timesteps, and information about the underlying grid and file conversion.

Walkthrough: Run CDO on the Cluster

  • This walkthrough will go through basic usage of CDO as outlined in their Tutorial Page.
  • sst.mon.mean.nc can be found here
  • PBS Script can be found here
  • You can transfer the files to your account on the cluster to follow along. The file transfer guide may be helpful.

Part 1: The PBS Script

#PBS -N cdoTest
#PBS -l nodes=1:ppn=2
#PBS -l pmem=4gb
#PBS -l walltime=3:00
#PBS -q force-6
#PBS -j oe
#PBS -o cdoTest.out

cd $PBS_O_WORKDIR
module load intel/15.0
module load cdo/1.9.5

# Display variables of a file
cdo -showname sst.mon.mean.nc
# Display number of timesteps of a file
cdo -ntime sst.mon.mean.nc
# Display Information about the underlying grid
cdo -griddes sst.mon.mean.nc
# File conversion with different file types: Copying whole data sets can be easily done with the copy operator. 
# With the '-f' switch, you can choose a new file type:
cdo -f grb -copy sst.mon.mean.nc sst.mon.mean.grb

  • The #PBS directives are standard, requesting 3 minutes of walltime and 1 node with 2 cores. More on #PBS directives can be found in the PBS guide
  • $PBS_O_WORKDIR is a variable that represents the directory you submit the PBS script from. Make sure the files you want to use are in the same directory you put the PBS script.
  • Output Files will also show up in this dir as well
  • module load nco/1.9.5 loads the 1.9.5 version of CDO. To see what version of a software are available, run module avail [Software], and load the one you want. The other module is a dependency that must be loaded before CDO is loaded.
  • The comment above each line in the PBS Script above explains what that line does.

Part 2: Submit Job and Check Status

  • Make sure you're in the dir that contains the PBS Script as well as the CDO program
  • Submit as normal, with qsub <pbs script name>. In this case qsub cdo.pbs
  • Check job status with qstat -t 22182721, replacing the number with the job id returned after running qsub
  • You can delete the job with qdel 22182721 , again replacing the number with the jobid returned after running qsub

Part 3: Collecting Results

  • In the directory where you submitted the PBS script, you should see a cdoTest.out file which contains the results of the job and sst.mon.mean.grb that was generated as an example of file conversion. Use cat or open the file in a text editor to take a look.
  • cdoTest.out should look like this:
---------------------------------------
Begin PBS Prologue Mon Jul 15 13:17:37 EDT 2019
Job ID:     26373952.shared-sched.pace.gatech.edu
User ID:    svemuri8
Job name:   cdoTest
Queue:      force-6
End PBS Prologue Mon Jul 15 13:17:37 EDT 2019
---------------------------------------
cdo showname: Processed 1 variable [0.01s 12MB]
 sst
cdo ntime: Processed 1 variable over 1542 timesteps [0.05s 13MB]
1542
cdo griddes: Processed 1 variable [0.01s 12MB]
#
# gridID 1
#
gridtype  = lonlat
gridsize  = 64800
xsize     = 360
ysize     = 180
xname     = lon
xlongname = "Longitude"
xunits    = "degrees_east"
yname     = lat
ylongname = "Latitude"
yunits    = "degrees_north"
xfirst    = 0.5
xinc      = 1
yfirst    = 89.5
yinc      = -1
cdo copy: Processed 99921600 values from 1 variable over 1542 timesteps [5.04s 21MB]
---------------------------------------
Begin PBS Epilogue Mon Jul 15 13:17:59 EDT 2019
Job ID:     26373952.shared-sched.pace.gatech.edu
User ID:    svemuri8
Job name:   cdoTest
Resources:  neednodes=1:ppn=2,nodes=1:ppn=2,pmem=4gb,walltime=00:03:00
Rsrc Used:  cput=00:00:00,energy_used=0,mem=0kb,vmem=0kb,walltime=00:00:22
Queue:      force-6
Nodes:
iw-c42-25.pace.gatech.edu
End PBS Epilogue Mon Jul 15 13:17:59 EDT 2019
---------------------------------------
  • You should also see a sst.mon.mean.grb file that is over 100 MB large in the working directory.
  • After the result files are produced, you can move the files off the cluster, refer to the file transfer guide for help.
  • Congratulations! You successfully ran CDO on the cluster.